16-58196420-A-G

Position:

• chr16-58196420-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001896.4(CSNK2A2):​c.216+313T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0705 in 152,214 control chromosomes in the GnomAD database, including 478 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.071 (478 hom., cov: 32)
• Consequence: CSNK2A2 NM_001896.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.804

Genes affected

CSNK2A2 (HGNC:2459): (casein kinase 2 alpha 2) This gene encodes the alpha', or alpha 2, catalytic subunit of the protein kinase enzyme, casein kinase 2 (CK2). Casein kinase 2 is a serine/threonine protein kinase that phosphorylates acidic proteins such as casein. It is involved in various cellular processes, including cell cycle control, apoptosis, and circadian rhythms. This heterotetrameric kinase includes two catalytic subunits, either alpha or alpha', and two regulatory beta subunits. The closely related gene paralog encoding the alpha, or alpha 1 subunit (CSNK2A1, Gene ID: 1457) is found on chromosome 20. An intronic variant in this gene (alpha 2) may be associated with leukocyte telomere length in a South Asian population. A related transcribed pseudogene is found on chromosome 11. [provided by RefSeq, Aug 2017]

CSNK2A2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BP6: Variant 16-58196420-A-G is Benign according to our data. Variant chr16-58196420-A-G is described in ClinVar as [Benign]. Clinvar id is 1228994.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CSNK2A2	NM_001896.4	c.216+313T>C		intron_variant		ENST00000262506.8	NP_001887.1
CSNK2A2	XM_047433626.1	c.216+313T>C		intron_variant			XP_047289582.1
CSNK2A2	XM_005255801.4	c.-192+313T>C		intron_variant			XP_005255858.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CSNK2A2	ENST00000262506.8	c.216+313T>C		intron_variant		1	NM_001896.4	ENSP00000262506.3
CSNK2A2	ENST00000565188.2	c.216+313T>C		intron_variant		2		ENSP00000454874.2
CSNK2A2	ENST00000562367.1	n.41+313T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0705 AC: 10716 AN: 152096 Hom.: 472 Cov.: 32

Gnomad AFR AF: 0.0550

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0484

Gnomad ASJ AF: 0.0574

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.0601

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0713

Gnomad OTH AF: 0.0630

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0705 AC: 10736 AN: 152214 Hom.: 478 Cov.: 32 AF XY: 0.0721 AC XY: 5364 AN XY: 74404

Gnomad4 AFR AF: 0.0550

Gnomad4 AMR AF: 0.0486

Gnomad4 ASJ AF: 0.0574

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.0601

Gnomad4 NFE AF: 0.0713

Gnomad4 OTH AF: 0.0695

Alfa AF: 0.0669 Hom.: 39

Bravo AF: 0.0668

Asia WGS AF: 0.173 AC: 598 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.8
DANN	Benign	0.86

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs77325010; hg19: chr16-58230324;